I'm 5'2" and the only off the rack bike I could get to fit was a Terry.

On the other hand I'm REALLY short waisted for my height, so we're probably not really comparable for anything except height.

Looking at the bike, I see it's a hybrid with an upright posture. Normally with that type of bike you wouldn't expect to see the kind of neck and shoulder pain you're talking about. That's more typical of a road bike with drop handlebars. Sometimes that sort of initial discomfort on a road bike will abate as you get used to riding with drop handlebars but that's clearly not what's going on here.

So. We have a hybrid and an upright posture. I see that the top tube length on that is 53.5 cm, that's 4.5 cm longer than my Terry Madeleine. On a hybrid, the kind of neck and shoulder pain you're talking about could be caused by having to reach too far forward. It could also be caused by the handlebars being too high or too low. On a hybrid it's ok for the handle bars to be anywhere from level with to a couple of inches above the seat, so you might check that. I had a lot of wrist and shoulder pain on a hybrid years ago because the frame was so badly skewed that the lowest level for the handlebars was about 4" ABOVE the seat even at full seat post extension (it was REALLY bad).

If the handlebars are ok for height, then it might be that forward reach is too long, which you can compensate for somewhat by using a shorter stem (bringing the handlebars back closer to the rider), but that requires a stem change and possibly an outlay of money if the bike shop won't swap it out for free, so check all other aspects of fit and adjustment first.

Check to make sure that your seat isn't tilted forward (or to the rear). It should be level. It'll take a level to be sure, too. You should be able to pick up a small level for under $5 if you don't already have one or you can't borrow one. A level will also help you figure out where the handlebars are with respect to the seat.

The seat tube angle on this bike is quite steep, I see that it's 75 degrees. It seems that many women are more comfortable with a lower angle, around 73 degrees or even a little less. I know of one woman on this forum who told me recently that when Terry changed the seat tube angle from 73 degrees to 74 in the model she was looking at, she couldn't ride the bike anymore, she just couldn't get comfortable on it. I don't know if there's a way to counteract that if that's a problem and I'm not actually sure if that's a likely culprit for neck/shoulder pain. I'll try to go look that posting up and ask the person specifically, or maybe she'll read this and chime in. This isn't something you can really change or compensate for.

Seat forward/aft position should also be checked. I can't remember off the top of my head exactly how to check that, it involves putting your foot on the pedal at a certain angle and then measuring from the front of the knee with a plumb-bob. Heck with it, here are a couple of pages with illustrations and instructions for checking all of these adjustments. Some of them require the help of a friend. I don't think the info about handlebar height is really applicable to a hybrid, but the third link is to a series of videos about fitting (specifically) a hybrid bike.

http://www.jimlangley.net/crank/bikefit.html
http://mikesbikes.com/page.cfm?PageID=22&tipid=30
http://www.ehow.com/video_2363020_hy...eight-fit.html

OK. so if you've checked seat level, seat height, saddle fore-aft position, and handlebar height, those are all the things I can think of on a bike that you can adjust without actually switching any parts out.

Sorry if this is kind of meander-y, I'm more or less thinking out loud.

OK so you mentioned not having padded shorts and seat discomfort. Padded shorts aren't so much for seat discomfort as they are about not sliding around in your shorts, eg the chamois is more for ANTI-FRICTION, particularly to protect you from friction due to the seams of the outer short. Yeah, they're a little bit for padding between you and the seat, but chamois in your shorts is not going to save you from an uncomfortable seat. Still it's worth getting a pair of lined shorts and trying them out before thinking about switching out the bike seat. Also, if you had to make any changes to seat position above, that may have already solved the seat issues.

If you've done all the tweaking to positioning that you can, you've gone out riding in your new chamois-lined shorts, and you're still having significant seat discomfort, now's the time to think about trying a different seat. You don't tell us what KIND of discomfort you're having from the saddle so I'm kind of guessing here. But I see that that saddle is very narrow and has no cutout. It actually looks more like a men's saddle to me, though it says it's WSD. If that seat is not working for you, try a different saddle with a cutout. Terry is one of the best manufacturers and designers for women's saddles. They have a 30 day return policy on their saddles, in other words you can try the saddle for 30 days and if it doesn't work for you, return it no questions asked. I would suggest you look more at recreational or all-purpose saddles, or maybe even touring saddles, since you're riding a hybrid.

PDF giving a side-by-side comparison of Terry's women's saddles:

http://terrybikes.forest.net/ftp/pub/2007_saddles.pdf

Link to Terry's womens saddles:

http://www.terrybicycles.com/saddles/womens

I hope that helps, even though it kind of disjointedly wanders all over the place.